Merge branch 'sean2' into 'master'

updated files for upload

See merge request !2

analysisScriptV1.R

+#[p]
+#Inititate the required libraries
+
+
+#[12]
+library(psych)
+library(plyr)
+library(reshape2)
+library(ggplot2)
+
+
+#[F]
+#Read in the data
+
+
+#[4]
+data <- read.csv("workshopRawData.csv") 
+
+
+#[E]
+#Convert dates
+
+
+#[11]
+data$Referral_Date <- as.Date(data$Referral_Date)
+data$Treat_Date <- as.Date(data$Treat_Date)
+
+
+#[L]
+#Check the data for errors
+#Missing data
+
+
+#[6]
+id_na <- sum(is.na(data$ID))
+age_na <- sum(is.na(data$Age))
+ref_na <- sum(is.na(data$Referral_Date))
+trt_na <- sum(is.na(data$Treat_Date))
+ser_na <- sum(is.na(data$Service_Name))
+
+
+#[A]
+#Category typos, ommissions and duplications
+
+
+#[16]
+id_uni <- unique(data$ID)
+age_uni <- unique(data$Age)
+ser_uni <- unique(data$Service_Name)
+
+id_dup <- count(data, 'ID')
+id_dup_sub <- subset(id_dup,id_dup$freq > 1)
+dups <- id_dup_sub$ID
+dupRows <- data[data$ID %in% dups,]
+
+
+#[C]
+#Incorrectly entered date stamps
+
+
+#[9]
+dataTime <- data
+dataTime$time_check <- dataTime$Treat_Date - dataTime$Referral_Date
+time_sub <- subset(dataTime, dataTime$time_check < 0)
+
+
+#[M]
+#Swap incorrectly entered date stamps
+
+
+#[2]
+time_rows <- as.integer(row.names(time_sub))
+for (i in 1:length(time_rows)){
+  # print(c("Before ",data[time_rows[i],]))
+  a <- data[time_rows[i],3]
+  b <- data[time_rows[i],4]
+  data[time_rows[i],3] <- b
+  data[time_rows[i],4] <- a
+  # print(c("After ",data[time_rows[i],]))
+}
+
+
+#[J]
+#Remove patients without team entries
+
+
+#[13]
+omiss <- subset(data, data$Service_Name == "")
+omiss_rows <- as.integer(row.names(omiss))
+dataClean <- data[-c(omiss_rows),]
+
+
+#[O]
+#Calculate the patient wait times
+
+
+#[8]
+dataClean$waitTime <- as.integer(dataClean$Treat_Date - dataClean$Referral_Date)
+waitDes <- describe(dataClean$waitTime)
+
+
+#[H]
+#Subset wait time data by month
+
+
+#[7]
+startDate <- min(dataClean$Referral_Date)
+endDate <- max(dataClean$Treat_Date, na.rm=TRUE)
+numMonths <- length(seq(from=startDate, to=endDate, by='month'))
+months <- seq(from=startDate, to=endDate, by='month')
+monthData <- list()
+waitList <- list()
+for (i in 1:(numMonths-1)){
+  a <- dataClean[which(dataClean$Treat_Date > months[i+1] &
+                         dataClean$Referral_Date < months[i+1]),]
+  monthData[[i]] <- a
+  waitList[[i]] <- data.frame(a$waitTime,a$Service_Name)
+}
+
+
+#[N]
+#Convert wait list into single multilevel dataframe
+
+
+#[5]
+dfWait <- melt(waitList)
+dfWait <- droplevels(dfWait)
+
+
+#[K]
+#Patient numbers barchart and descriptives
+
+
+#[14]
+waitListTab <- table(dfWait$L1)
+waitListDf <- as.data.frame(waitListTab)
+waitListDes <- describe(waitListDf$Freq)
+barplot(waitListTab, xlab="Month", ylab="Frequency",
+        main="Number of patients on the waiting list",
+        cex.names = 0.8)
+
+
+#[G]
+#Patient numbers by team barchart and descriptives
+
+
+#[10]
+teamWaitListTab <- table(dfWait$a.Service_Name,dfWait$L1)
+teamWaitListDf <- as.data.frame(teamWaitListTab)
+teamWaitListDes <- describeBy(teamWaitListDf$Freq,teamWaitListDf$Var1)
+barplot(teamWaitListTab,beside=TRUE, xlab="Month", ylab="Frequency",
+        main="Number of patients on the waiting list by team",
+        cex.names = 0.8, legend=TRUE,
+        args.legend=list(x="topright", legend=c("Team 1", "Team 2")))
+abline(h=mean(teamWaitListTab[1,]))
+abline(h=mean(teamWaitListTab[2,]), lty=2)
+
+
+#[I]
+#Patient waiting times boxplot and descriptives by month
+
+
+#[1]
+timeWaitTimePlot <- qplot(factor(L1), value, data=dfWait, geom='boxplot')
+timeWaitTimePlot + xlab("Month") + ylab("Waiting time (days)") +
+  ggtitle("Patient waiting times for service X over time")
+waitTimeDes <- describeBy(dfWait$value,group=dfWait$L1)
+
+
+#[B]
+#Patient waiting times boxplot and descriptives by team
+
+
+#[3]
+teamWaitTimePlot <- qplot(a.Service_Name,value, data=dfWait, geom='boxplot')
+teamWaitTimePlot + xlab("Month") + ylab("Waiting time (days)") +
+  ggtitle("Patient waiting times for service by team")
+teamWaitTimeDes <- describeBy(dfWait$value, group=dfWait$a.Service_Name)
+
+
+#[D]
+#Patient waiting times boxplot and descriptives by month and team
+
+
+#[15]
+dfWait$ServTime <- interaction(dfWait$a.Service_Name,dfWait$L1)
+breaks <- c("Team1.1","Team1.2","Team1.3","Team1.4","Team1.5",
+            "Team1.6","Team1.7","Team1.8","Team1.9","Team1.10",
+            "Team1.11","Team1.12","Team1.13","Team1.14","Team1.15",
+            "Team1.16","Team1.17","Team1.18","Team1.19","Team1.20",
+            "Team1.21","Team1.22","Team1.23")
+lab <- as.character(seq(1,23))
+teamTimeWaitTimePlot <- qplot(factor(ServTime), value, data=dfWait, fill=a.Service_Name,
+                              geom='boxplot')
+teamTimeWaitTimePlot + scale_x_discrete(name="Month", breaks=breaks, labels=lab) +
+  ylab("Waiting Time")
+teamTimeWaitTimeDes <- describeBy(dfWait$value, group=list(dfWait$a.Service_Name,dfWait$L1))
+
+
+
+
+
+
+

analysisScriptV2.R

+#[B]
+#Inititate the required libraries
+
+
+#[7]
+library(psych)
+library(plyr)
+library(reshape2)
+library(ggplot2)
+
+
+#[C]
+#Read in the data
+
+
+#[13]
+data <- read.csv("workshopRawData.csv")
+
+
+#[G]
+#Get list of column names
+
+
+#[2]
+name_list <- function(data){
+  nList <- as.list(colnames(data))
+  print("The structure of the data is as follows")
+  print("Any dates will need to be converted from factor to Date format")
+  str(data)
+  return(nList)
+}
+nList <- name_list(data)  #Inputs: dataframe
+
+
+#[I]
+#Convert dates
+
+
+#[15]
+convertDates <- function(data, cols){
+  for (i in 1:length(cols)){
+    data[[cols[i]]] <- as.Date(data[[cols[i]]])
+    print(paste("data column",cols[i],"converted to Date format"))
+  }
+  
+  return(data)
+}
+data <- convertDates(data, c(3,4))  
+#Inputs: dataframe, columns to be converted to date format
+
+
+#[F]
+#Check the data for errors
+#Missing data
+
+
+#[3]
+missing_data <- function(data){
+  colsN <- colnames(data)
+  cols <- seq(1, length(colsN))
+  missList <- list()
+  for (i in 1:length(cols)){
+    missList[i] <- sum(is.na(data[[cols[i]]]))
+    if (missList[i] > 0){
+      print(paste("In column",cols[i],"there are",missList[i],"missing data points"))
+    }
+  }
+  return(missList)
+}
+missList <- missing_data(data)  #Inputs: dataframe
+
+
+#[K]
+#Category typos, ommissions and duplications
+
+
+#[9]
+typo_check <- function(data,cols){
+  typoList <- list()
+  for (i in 1:length(cols)){
+    typoList[[i]] <- unique(data[[cols[i]]])
+    print(paste("There are",length(typoList[[i]]),"unique entries in column",cols[i]))
+  }
+  return(typoList)
+}
+typoList <- typo_check(data, c(1,2,5))  
+#Inputs: dataframe, columns to check for number of unique categories
+
+dup_check <- function(data,nList,idCol){
+  idName <- nList[[idCol]]
+  id_dup <- count(data, idName)
+  id_dup_sub <- subset(id_dup,id_dup$freq > 1)
+  dups <- id_dup_sub[[idCol]]
+  dupRows <- data[data[[idCol]] %in% dups,]
+  print("The rows with duplicated ID's are...")
+  print(dupRows)
+  return(dupRows)
+}
+dupRows <- dup_check(data,nList,1)
+#Inputs: dataframe, list of column names, column containing unique ID's
+
+
+#[M]
+#Incorrectly entered date stamps
+
+
+#[11]
+date_check <- function(data){
+  dataTime <- data
+  dataTime$time_check <- dataTime$Treat_Date - dataTime$Referral_Date
+  time_sub <- subset(dataTime, dataTime$time_check < 0)
+  print("The following rows likely have incorrectly entered date stamps...")
+  print(time_sub)
+  return(time_sub)
+}
+time_sub <- date_check(data)  #Inputs: dataframe
+
+
+#[L]
+#Swap incorrectly entered date stamps
+
+
+#[14]
+correct_dates <- function(data,time_sub,dColOne,dColTwo){
+  time_rows <- as.integer(row.names(time_sub))
+  for (i in 1:length(time_rows)){
+    print("The entries")
+    print(data[time_rows[i],])
+    a <- data[time_rows[i],dColOne]
+    b <- data[time_rows[i],dColTwo]
+    data[time_rows[i],dColOne] <- b
+    data[time_rows[i],dColTwo] <- a
+    print("Have been changed to")
+    print(data[time_rows[i],])
+  }
+  return(data)
+}
+data <- correct_dates(data,time_sub,3,4)
+#Inputs: dataframe,
+#subset dataframe of rows with incorrectly entered timestamps,
+#column with referral date, column with treatment date
+
+
+#[H]
+#Remove patients without team entries
+
+
+#[1]
+omission_removal <- function(data,cols,targets){
+  for (i in 1:length(cols)){
+    for (j in 1:length(targets)){
+      omiss <- subset(data, data[[cols[i]]] == targets[j])
+      omiss_rows <- as.integer(row.names(omiss))
+      dataClean <- data[-c(omiss_rows),]
+      print("The following rows have been removed")
+      print(data[omiss_rows,])
+    }
+  }
+  return(dataClean)
+}
+dataClean <- omission_removal(data,c(5),c(""))  
+#Inputs: dataframe, column(s) to check for targets, target(s)
+
+
+#[E]
+#Calculate the patient wait times
+
+
+#[18]
+calc_wait <- function(dataClean,dateCols){
+  dataClean$waitTime <- as.integer(dataClean[[dateCols[2]]] - dataClean[[dateCols[1]]])
+  print("The wait time column has been added to the dataframe dataClean")
+  return(dataClean)
+}
+dataClean <- calc_wait(dataClean,c(3,4))  
+#Inputs: dataframe, columns to calculate wait times
+
+
+#[Q]
+#Generate wait time descriptives and histogram - Aggregate
+
+
+#[12]
+top_level_des <- function(dataClean,colNum){
+  waitDes <- describe(dataClean[colNum])
+  write.csv(waitDes,"top_level_descriptives.csv")
+  jpeg("wait_time_hist.jpeg")
+  waitHist <- hist(dataClean[[colNum]],main="Frequency of wait times for all patients",
+                   xlab="Wait time")
+  dev.off()
+}
+top_level_des(dataClean,6)  #Inputs: dataframe, column to describe and plot
+
+
+#[A]
+#Subset wait time data by month 
+#(patients treated and still awaiting treatment during a given month)
+
+
+#[17]
+data_monthly <- function(dataClean,refDate,treatDate){
+  startDate <- min(dataClean[,refDate])
+  endDate <- max(dataClean[,treatDate], na.rm=TRUE)
+  months <- seq(from=startDate, to=endDate, by='month')
+  numMonths <- length(months)
+  waitList <- list()
+  errorCount <- 0
+  for (i in 1:(numMonths-1)){
+    a <- dataClean[which(dataClean[[treatDate]] > months[i] &
+                           dataClean[[refDate]] < months[i+1]),]
+    actWait <- rep(0,length(a[[1]]))
+    for (j in 1:length(a[[1]])){
+      if (a[j,treatDate] < months[i+1]){
+        actWait[j] <- a[j,treatDate] - a[j,refDate]
+      }else {
+        actWait[j] <- months[i+1] - a[j,refDate]
+      }
+      if (actWait[j] < 0){
+        errorCount <- errorCount+1
+        print("Negative value in month",i,"row",j)
+      }
+    }
+    a$activeWaitTime <- actWait
+    waitList[[i]] <- data.frame(a$activeWaitTime,a$Service_Name)
+  }
+  if (errorCount > 0){
+    print(paste("Warning:",errorCount,"negative values detected check the output"))
+  } else{
+    print("Calculations completed. No negative values detected")
+  }
+  return(waitList)
+}
+waitList <- data_monthly(dataClean,3,4) #Inputs: dataframe, referral date column,
+                                        #treatment date column
+
+
+#[D]
+#Convert wait list into single multilevel dataframe
+
+
+#[5]
+convert_list <- function(waitList){
+  dfWait <- melt(waitList)
+  dfWait <- droplevels(dfWait)
+  print("The column names for the analysis are...")
+  print(colnames(dfWait))
+  return(dfWait)
+}
+dfWait <- convert_list(waitList)  #Inputs: dataframe
+
+
+#[P]
+#Patient numbers barchart and descriptives
+
+
+#[6]
+patient_nums <- function(dfWait,addDate){
+  waitListTab <- table(dfWait$L1)
+  waitListDf <- as.data.frame(waitListTab)
+  waitListDes <- describe(waitListDf$Freq)
+  if (addDate == 1){
+    write.csv(waitListDes,paste(Sys.Date(),"wait_list_numbers_monthly_des.csv",
+                                sep="_"))
+    jpeg(paste(Sys.Date(),"wait_list_numbers_monthly.csv",sep=""))
+  }else{
+    write.csv(waitListDes,"wait_list_numbers_monthly_des.csv")
+    jpeg("wait_list_numbers_monthly.jpeg")
+  }
+  barplot(waitListTab, xlab="Month", ylab="Frequency",
+          main="Number of patients on the waiting list",
+          cex.names = 0.8)
+  dev.off()
+}
+patient_nums(dfWait,1)  #Inputs: dataframe, use 1 to add todays date to filenames
+
+
+#[R]
+#Patient numbers by team barchart and descriptives
+
+
+#[16]
+team_patient_nums <- function(dfWait){
+  teamWaitListTab <- table(dfWait$a.Service_Name,dfWait$L1)
+  teamWaitListDf <- as.data.frame(teamWaitListTab)
+  teamWaitListDes <- describeBy(teamWaitListDf$Freq,teamWaitListDf$Var1)
+  teamWaitListDes <- do.call(rbind.data.frame,teamWaitListDes)
+  jpeg("team_wait_list_numbers_monthly.jpeg")
+  barplot(teamWaitListTab,beside=TRUE, xlab="Month", ylab="Frequency",
+          main="Number of patients on the waiting list by team",
+          cex.names = 0.8, legend=TRUE,
+          args.legend=list(x="topright", legend=c("Team 1", "Team 2")))
+  abline(h=mean(teamWaitListTab[1,]))
+  abline(h=mean(teamWaitListTab[2,]), lty=2)
+  dev.off()
+  write.csv(teamWaitListDes,"team_wait_list_numbers_monthly_des.csv")
+}
+team_patient_nums(dfWait) #Inputs: dataframe
+
+
+
+#[J]
+#Patient waiting times boxplot and descriptives by month
+
+
+#[8]
+time_patient_wait_time <- function(dfWait){
+  jpeg("wait_times_monthly.jpeg")
+  timeWaitTimePlot <- qplot(factor(L1), value, data=dfWait, geom='boxplot')
+  timeWaitTimePlot + xlab("Month") + ylab("Waiting time (days)") +
+    ggtitle("Patient waiting times for service X over time")
+  dev.off()
+  waitTimeDes <- describeBy(dfWait$value,group=dfWait$L1)
+  waitTimeDes <- do.call(rbind.data.frame,waitTimeDes)
+  write.csv(waitTimeDes,"wait_times_monthly_des.csv")
+}
+time_patient_wait_time(dfWait)  #Inputs: dataframe
+
+
+#[N]
+#Patient waiting times boxplot and descriptives by team
+
+
+#[10]
+team_patient_wait_time <- function(dfWait){
+  jpeg("wait_times_team.jpeg")
+  teamWaitTimePlot <- qplot(a.Service_Name,value, data=dfWait, geom='boxplot')
+  teamWaitTimePlot + xlab("Month") + ylab("Waiting time (days)") +
+    ggtitle("Patient waiting times for service by team")
+  dev.off()
+  teamWaitTimeDes <- describeBy(dfWait$value, group=dfWait$a.Service_Name)
+  teamWaitTimeDes <- do.call(rbind.data.frame,teamWaitTimeDes)
+  write.csv(teamWaitTimeDes,"wait_times_team_des.csv")
+}
+team_patient_wait_time(dfWait)  #Inputs: dataframe
+
+
+#[O]
+#Patient waiting times boxplot and descriptives by month and team
+
+
+#[4]
+team_time_patient_wait_time <- function(dfWait){
+  dfWait$ServTime <- interaction(dfWait$a.Service_Name,dfWait$L1)
+  breaks <- dfWait$ServTime[seq(1,length(levels(dfWait$ServTime)),2)]
+  lab <- as.character(seq(1,length(breaks)))
+  jpeg("wait_times_monthly_team.jpeg")
+  teamTimeWaitTimePlot <- qplot(factor(ServTime), value, data=dfWait,
+                                fill=a.Service_Name, geom='boxplot')
+  teamTimeWaitTimePlot + scale_x_discrete(name="Month", breaks=breaks, labels=lab) +
+    ylab("Waiting Time")
+  dev.off()
+  teamTimeWaitTimeDes <- describeBy(dfWait$value,
+                                    group=list(dfWait$a.Service_Name,dfWait$L1))
+  teamTimeWaitTimeDes <- do.call(rbind.data.frame,teamTimeWaitTimeDes)
+  write.csv(teamTimeWaitTimeDes,"wait_times_monthly_team.csv")
+}
+team_time_patient_wait_time(dfWait) #Inputs: dataframe
+
+
+